Hierarchical and spatially explicit clustering of DNA sequences with BAPS software
Autor: | Thomas R. Connor, Lu Cheng, Jukka Corander, Jukka Sirén, David M. Aanensen |
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Rok vydání: | 2013 |
Předmět: |
Bayesian probability
Population Bayesian inference evolutionary epidemiology Biology computer.software_genre Evolution Molecular 03 medical and health sciences Bayes' theorem Software Genetics Cluster analysis education Molecular Biology Ecology Evolution Behavior and Systematics 030304 developmental biology 0303 health sciences education.field_of_study 030306 microbiology business.industry Bayes Theorem Sequence Analysis DNA genetic population structure Resources Hierarchical clustering ComputingMethodologies_PATTERNRECOGNITION Genetics Population Borrelia burgdorferi phylogeographics DECIPHER Data mining business computer |
Zdroj: | Molecular Biology and Evolution |
ISSN: | 1537-1719 |
Popis: | Phylogeographical analyses have become commonplace for a myriad of organisms with the advent of cheap DNA sequencing technologies. Bayesian model-based clustering is a powerful tool for detecting important patterns in such data and can be used to decipher even quite subtle signals of systematic differences in molecular variation. Here, we introduce two upgrades to the Bayesian Analysis of Population Structure (BAPS) software, which enable 1) spatially explicit modeling of variation in DNA sequences and 2) hierarchical clustering of DNA sequence data to reveal nested genetic population structures. We provide a direct interface to map the results from spatial clustering with Google Maps using the portal http://www.spatialepidemiology.net/ and illustrate this approach using sequence data from Borrelia burgdorferi. The usefulness of hierarchical clustering is demonstrated through an analysis of the metapopulation structure within a bacterial population experiencing a high level of local horizontal gene transfer. The tools that are introduced are freely available at http://www.helsinki.fi/bsg/software/BAPS/. |
Databáze: | OpenAIRE |
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